All the time in Hiroshi Strange Love, with Professor Iaizawa complaining about how his face is cut out, wondering when things got so serious, asking where the government got the "World Domination" style picture of him, proclaiming the coming sequel, talking about how he hopes they become an anime, etc.
In the Black Cat manga, Sven does this literally when he bangs his head on the edge of the panel in surprise, cracking the page.
Excel Saga. It would probably be easier to mention all the scenes this trope wasn't in...!
In Fushigi Yuugi, when Miaka is told to remove her clothes as part of a test to see if she is worthy of receiving a magical relic, she strips down to her one-piece underclothes, then comments "This is the limit of what the broadcast code allows."
Mazinger Z: The original manga penned by Go Nagai broke the fourth wall several times. In one of the first episodes Kouji gets forced to kill a Mook in self-defense and he suffers s Heroic BSOD thinking he is a murderer... until another character calms him down stating he was only defending himself and he is the main character and The Hero, so he did no wrong. And in this page Count Brocken complains Kouji fights dirty and yells the main character should not fight dirty and the fans will cry. Kouji was not impressed.
Throughout the manga, there are extra comics about the characters reactions and hopes about a popularity poll. This includes discussions about how much 'screen time' they've had in recent chapters and at one point Scar using alchemy to blow up the author when he reads that he has tied with her way low on the poll.
And the side story where Ed and Mustang have a fight.
"Hughes: We don't have many pages left, so let's get it going!"
In the 2003 series Hughes asks Mustang why he called him just to seemingly pester him. Mustang replies that it's because it had been a while since his last appearance, followed by a cut to his office with Roy and the entirety of Team Mustang staring at the camera.
While generally not appearing in the anime, the manga series for Tenchi Muyo! featured quite a few references to episodes of the OVA, as well as Aeka stopping a bit of it by screaming at Ryoko and Washu to, in the English translation, 'stop this Brecht crap!'; the two lackadaisically agree to return to the story.
In episode 96 of Ranma ˝ after yet another dreary conclusion Ranma pointedly asks...
"Speaking of which, what was the point of this episode again?"
The manga had one moment where Mariko uses several moves reminiscient of young Goku in Dragon Ball (extending baton, standing on a "cloud" made of pompoms). Ranma demands to know which manga she thinks she's in.
Jessie, James, and Meowth in Pokémon occasionally show awareness that they're cartoon villains. In Pokémon 2000, they even proudly and dramatically declare their presence on the big screen, to which the annoyed Ash retorts, "I'll just catch this on video!" The Slowking from the same film also breaks the fourth wall by telling Team Rocket how people have been watching their sudden switch to heroism the entire film.
Later in the same film, they mention diamonds and pearls again, and Meowth comments, "Let's get through this season first."
Lampshaded in "The Whistle Stop", when Meowth comments about what would happen to them after the bridge falls: "We usually don't wash out this early in the episode!"
One Pikachu short trailer had Meloetta winking at the camera.
In Pokémon 3, Meowth asks Jesse and James if they'll get a bigger part in the next movie.
Ash and his pals rarely acknowledge the presence of the fourth wall, but the intro for one Season 1 episode ended with Brock breaking up an argument between Ash and Misty by saying they had to start the show because they were running late, and Pikachu waving at the audience.
In the Intercontinuity Crossover with Detective Conan, Lupin thinks he's about to get lucky with Fujiko. He turns to the camera and announces "To you 80 million adult viewers: thank you for your patience!" and pounces on her. The same movie mixes this with Leaning on the Fourth Wall regarding the crossover nature of the story. Detective Conan has previously established that Lupin III manga exists in their world. Zenigata thinks it's odd that Koguro, a professional detective, doesn't know about Lupin. Koguro says that he always just thought that Lupin was a comic book character.
At the end of the penultimate arc of Higurashi no Naku Koro ni Kai, when trying to figure out why their efforts failed, Rena says she understands why, looks straight out at the screen and says, "Did you really believe?" It turns out that she's talking to Hanyuu, who then affirms her desire to finally fight alongside them, but the double meaning seems clear.
This is even more prevalent in the final episode of the game, where Rika (maybe) directly speaks to the player, saying that the task of getting the Good End is monumentally hard and he must not be overcome by despair, because it's despair that kept them locked in the "Groundhog Day" Loop until then. Like in the anime, she explains that Fate can be defeated only if everyone believes, including you. And she even adds that if you give up and uninstall the game, they will stay trapped in the Downer Ending. Forever.
The sequel-of-sorts, Umineko no Naku Koro ni, has Bernkastel (who may or may not be an incarnation of Rika's) occasionally addressing the readers directly as well.
Featherine, despite being a character inside the game, can reach out and edit the visual novel at will.
In the series Cafe Kichijouji De when Hifumi Minagawa walks in with pink hair during the colour pages and everyone asks "What's with your hair?" He replies "What do you mean? It's been like this the last two chapters, but no body noticed because the Manga is in black and white,"
He goes on to say "The boss' hair is thinning too, but even he doesn't know because the artist only draws lines" to which Taro and Maki ask "Who's drawing lines?!"
In one episode of Martian Successor Nadesico, Izumi makes yet another pun. This one, however, makes use of such an obscure, outdated word that some of the characters have to explain to the others what in the world she was talking about. The scene ends with Megumi looking directly into the "camera" and saying, "We've learned something today, haven't we?" The others then ask her who she's talking to, a question she completely ignores.
In the dub, she actually answers the question with "The fourth wall!"
The Houshin Engi manga has the occasional Breaking the Fourth Wall moment. For example, one villain advises the readers to look up the difference between strategy and tactics in a dictionary after saying he favors the former over the latter in war.
Pulled once in Air Gear during the battle with the Night King gang. When Emily explains to the reader/viewer how the track team was able to move the shed to trap Buccha, Yayoi quickly asks her "Who are you explaining this to?"
In the manga version of Kare Kano, when Kazuma's band crashes the school festival and the narrator starts spouting a bunch of stock rock and roll manga cliches, Yukino appears with a very cynical look and says "When did this become a rock manga?"
Keroro Gunsou has had episodes where the characters have conversations with the narrator. This has also happened in the manga.
The Omake at the end of one of the Filler arcs of Bleach is made entirely of this. It shows Ichigo teleporting back into the main story, at which point Nel asks him if the corporate guys said he could come back. Then Orihime shows up with the corresponding volume of the manga and tells him "go to this scene".
It's actually a running gag. At the start of the next filler, Ulquiorra stops his fight with Ichigo and sits down to have a sip of tea. When Ichigo asks why, Ulquiorra tells him that the studio execs will be cutting to something different for a little while. Nel then appears and asks the audience to "just bear with us here." They also ran a similar omake at the end of the filler.
And then later in the couple of episodes focusing on the Kakura Rizer team, Ishida pops up, and offers this gem, whilst explaining about various abilities.
Ishida: While in that state, she gains the ability to use several techniques that we can't air on TV.
During the Hueco Mundo arc, after Mayuri Kurotsuchi's victory against Szayel Aporro Granz, Captain finds his lieutenant and (sort of) daughter Nemu Kurotsuchi lying on the ground without a sign of life. He bends over and... does some unknown, yet very embarrassing actions for anyone who saw them (Renji Abarai and Uryuu Ishida, to be precise). In both manga and anime they ask "which part of those movements involved any kind of healing?!", yet only in the anime Ishida said that those actions were impossible to air on TV. Mayuri not only responded, that those actions were only as perverted as "they" saw them, but also helped in Breaking The Wall. Also during this battle, when Pesche Gautiche reveals his zanpakutou and likens it to Seele Schneider, Uryuu denies the similarities. This leads to Pesche's angered rant about how his "thingy" is "way thicker and more useful than Uryuu's thingy". This soon cuts out to a "Technical difficulties" screen featuring Dondochakka.
When Noba zips his mask after being approached by Rangiku, Ururu turns to the audience and explains: "He's a little shy."
During the Zanpakto unknown tales saga, in one of the episode previews, Ichigo asks why Kenpachi's zanpakto hadn't materialized. The conversation continues with:
"Idiot! If Kenpachi's zanpakto materialized, Soul society would be wiped from existence and the show would be over!"
"So the studio stepped in huh?"
In short, the Bleach anime is fond of breaking the fourth wall. However, it never happens in the manga.
With the exception of Aizen's Shikai/Bankai powers. Explicitly that anyone who sees his Bankai falls under the complete hypnosis of his Shikai and the only shinigami not to have seen it is Ichigo. This is fine and all right up until the point where Aizen tricks Hitsugiya into stabbing Momo. Not any of the captains nor the audience themselves see or hear Ichigo screaming at Hitsugiya to stop until it's too late
THE iDOLM@STER - Subverted/Played with in a In-Universe example, with Haruka mentioning the script during the Are we live? show and with Ami and Mami commenting about the report during the Ramen segment with Takane.
The last episode of Bastard!! has Arshes Nei asking Gara why he hasn't won the fight with the giant monster yet, prompting him to explain that "It's no fun to win while offscreen!" He then turns to the camera and says "OK folks. Watch this." before unleashing his most powerful attack.
There's multiple instances of this in the manga, such as Lars freaking out that the story content is much too sexy for its rating, and Dark Schneider commenting about what he's gonna do with his censored penis.
In the Strawberry Marshmallow manga, the prologue to episode 2 begins with Chika sitting in a wastebasket. We go back 30 minutes to see the events leading up to this predicament, after which she tells the viewer, "...and that's how it all happened." Miu asks, "You say something?"
In the prologue to episode 3, she tells the prematurely-appearing "The End", "No! Not 'The End'!"
In episode 5, Nobue says "A 16-year-old girl shouldn't be smoking." But she's not facing Chika, she's facing the reader.
Akahori Gedou Hour Rabuge had Akumako stating that "this anime has only three episodes left! We don't know if we may get a second season!".
Sonic X does it a few times, particularly Charmy finding out what happened when the Chaotix team were away by watching Sonic X on DVD, Eggman becoming the "main character" of the series and renaming the show Eggman X, and Eggman denying Sonic's claim that he (Sonic) is the main character.
Consecutive to the DVD scene above, the Chaotix introduce themselves directly to the audience. After Vector and Espio finish up, Charmy is ready to start when Vector informs him that they're low on time. Charmy tries to start his introduction anyway, and is promptly cut off by a commercial.
Only in the dub - in the original, the Eyecatch features his information.
Done several times in Slayers, mostly in the first season of the anime. Near the end of that season, Lina lampshades her lack of screentime during her 'Pretty Lina's Magic Lesson'. Zelgadis and Gourry also mention the ridiculous things that happen during serious moments, such as Zelgadis citing how "they" (the writers) can't keep one episode too serious for too long. After that season, however, the fourth wall-breaking stopped.
Also done in Niji Iro Togarashi. When Shichimi asks the landlord who his father is (considering that The father had many wives, including Shichimi's mother, I doubt it's going to be a happy reunion), the landlord replies that he can't tell Shichimi who his father is yet because it's only the first chapter and that he should really respect the mangaka's wishes.
In the first episode's "In the Next Episode" sequence in Fumoffu, Sousuke informs the viewers that the next episode will be featuring the giant armed suits "Armed Slaves" before Kaname shoots that down because Fumoffu was going to be a high-school romantic comedy.
The Full Metal Panic! manga has frequent references to the fact that it's a comic (eg. "I said that three chapters ago!")
The manga version of He Is My Master is made entirely of this trope; the Author Avatars are essentially main characters at this point that regularly interact with the rest of the cast.
Gintama uses this a lot. Possibly the most triumphant example of this trope: Otae jumped out of the TV to kill the author because she was pissed off that the gorilla was more popular with fans than her. The anime promptly gets screwed up and stopped airing altogether, until the studio staff rebuilt a robotic replacement of the author.
In FLCL, Naota looks to the audience and says "Do you find this as confusing as I do?"
Yes, yes we do.
From Kamon: "That's enough now, huh? Let's just stay with anime. It's hard to be in manga form. It takes time and is a lot of work. After the first episode they said not to do the manga thing again, but then we get accused of being lazy, right?" And later, "...what does fooly cooly mean? ...come on, you have to know, the main character always knows stuff like that."
After Kamina declares his plan to hijack a ganmen and pilot it through sheer force of will in the second episode of Tengen Toppa Gurren Lagann, Yoko turns to the camera and says, "Where does he get his confidence from?"
In chapter 226 of Mahou Sensei Negima!, Rakkan has stolen the panties of one of two girls who have imprisoned him and several of Negi's friends in a dimensional trap. In order to draw the girls out of hiding he begins... enjoying the panties in a rather perverted manner. As he threatens to lick them, Konoka holds up a "please stand by" card to the reader while telling Rakkan, "You can't go any further than that... There are children reading this!" Later, Konoka murmurs, "Are we really allowed to show this?"
In the first episode of the Saber Marionette J sequel Saber Marionette J To X, Hanagata (upon being punched through a roof and into the sky) proudly announces to the audience that this is his first appearance and flight in the new series. The exact opposite was true in the final episode of J to X when Hanagata proudly announces to the audience that it is his last flight in the series.
Also in the manga, when Lime wakes up for real and she and Otaru... erm... get acquainted, he suggests her to get dressed because "this is a shonen manga".
Later in the same episode, Tohru comments, "Somehow this has turned into a fighting anime."
In one chapter of the manga Bizenghast, when asked, "Do you see that?" the quirky spirit Edaniel looks up out of the page and reacts with shock: "There are people reading this book!"
Though the main series had none, Neon Genesis Evangelion had a few in the extras (you ran out of ink too, didn't you ya bastards!)
End of Evangelion had a treat for those who went to see the premiere. Near the end of the movie there's a host of live action clips, including an empty theatre. Gainax, get this, shot footage of the same theatre where the film screened when it filled with otaku and then spliced it in. Break them walls down.
At one point in the recent third series of OVAs for Tenchi Muyo!, Washuu takes a moment to explain things to the viewers at home, and is complimented for doing so by the Lady Seto.
In one episode of Noir Mirielle hums along with the soundtrack that's playing while she's cutting Kirika's hair.
The Gag Dub of Ghost Stories positively mauls its fourth wall, breaking it more and more as the series goes on. Characters identify plot points, comment on how they're being animated (usually poorly), and wonder which movie they're ripping off for a given episode's plot (especially that they meet so many villains who look like Samara from The Ring). In one episode towards the end of the series they conflate Satsuki's father with his voice actor, Illich Guardiola, and call him "Illich" for the rest of the episode. Maybe it's safe to say this show has no wall whatsoever.
In one episode of D.N.Angel, the eyecatch typically used before and after commercials is farcically placed at major scene changes as well, prompting Riku and Risa to yell, "Enough already!" after half a dozen appearances.
In an interesting variation, in Princess Tutu, Princess Kraehe breaks the internal fourth wall at one point by speaking directly to Drosselmeyer. The latter is very put off by this.
It's touched on in the last episode when Drosselmeyer wonders if he's in someone else's story.
In Detective Conan, Conan makes frequent internal asides to the viewer, such as when Mouri Kogoro talks about all the cases he's solved and Conan thinks to the camera, "Oi oi, I'm the one who solved those."
In the opening narration of the Non-Serial MovieCrossroads in the Ancient Capital, Heiji Hattori is talking to the camera about the series's backstory when his girlfriend Kazuha comes up and asks him who he's talking to. When Heiji says he's explaining things to the audience, Kazuha thinks he's just being silly.
In Sketchbook Tanabe Ryou and Himuro Fuu seem to have this ability, but it is hard to tell, as their whole school life seems to be a comedy stage to them, and they might just be speaking to an imaginary audience.
In Part 3 of JoJo's Bizarre Adventure it looks like the hero has died. The foe who slew him begins to brag out of the blue that he caused an early finish to that Part. Then the hero is revealed to be alive after all, and speaks about how he will not be replaced by his supposed killer as protagonist of the series.
In Katekyo Hitman Reborn!, as Belphegor is describing the fights between himself and his brother, Flan remarks to the viewers concerning knife throwing 'It's dangerous, so good little kids shouldn't try it at home.' This is then lampshaded when Bel then says 'Who are you talking to?!"
The whole "Lucky Channel" segment of Lucky Star anime (no, the manga does not have this) implies that the series is just a TV show produced by fictional TV channel Lucky Channel. During these segments, the 2 staffs of Lucky Channel, Minoru and Akira, speak to the audiences and act like the characters are just acting in their show. This also happen in the OVA.
Also, Misao does this in the OVA, first with her statement "We'll show them the true power of minor characters!" and after the match she sighs "It seems minor character aren't meant to win."
In the 8th chapter of the Dragon Ball manga, Akira Toriyama used an unusual (for manga) way of breaking the fourth wall. Son Goku sends Yamcha into the air with his punch, but Yamcha bounces off the frame's border back to the ground.
In later chapters there are a few instances, where different characters refers to the fact that it's a manga, such as discussions of acceptableness of dirty jokes in the manga for children.
The Buu saga featured a scene where Kuririn realized that the panels showing Goten's and Trunks's Fusion Dance were being photocopied and criticized robot Akira Toriyama (the series creator) for his laziness. Toriyama even said to his editor that he didn't need to pay him for this page. After that, he disappeared off the face of the Earth. Naturally, this scene isn't in the anime. (Not like Toei doesn't reuse animation or anything...)
There is also at least one blatant breaking of the fourth wall in the anime. In Episode 205, "I'll Fight Too", Krillin is shown for the first time (outside of the opening and closing credits) with a full head of hair. Gohan then immediately turns to the camera, gesturing his thumb back at Krillin, and tells the audience that Krillin has stopped fighting and has also stopped shaving his head. Though that happened in the manga as well.
Also, in Episode 287, "Celebrations with Majin Buu", Vegeta says, "What are you looking at?" in response to the narrator implying he is not having fun at the party.
Fat Buu does this at one point, asking the viewers to smell his breath.
Dororo does this several times. Author Osamu Tezuka getting crushed by a rain of rocks summoned by a demon while at his drawing board. Later, when a mysterious voice speaks to him, Dororo asks the reader if it was him/her. And when Dororo is embarrassed, he asks the writer to stop showing this part.
Also happens in other works of Tezuka; he appears in a Special of Black Jack as a stressed-out manga artist drawing at a table in a bar. Pinoko rushes in and causes him to spill coffee all over his hard work, much to his dismay. And in another instance in Black Jack manga, a character falls and hits the panels of the manga page
The English broadcast of Cat Ninja Legend Teyandee - Samurai Pizza Cats - constantly involved the narrator conversing with the cast and commenting on the Japanese attributes such as the written language and sight gags, and made complaints to the writers and producers regarding strange plots.
"It's bad enough I have jerk Britain laughing at me without suffering these little animated insert thingies!"
Iceland breaks the fourth wall when he introduces himself at the beginning of The Movie. During the Hetaween 2011 event, he also tells the audience to stop staring at him.
In the 3rd episode of Rosario + Vampire, succubus Kurumu does this when she is treating Tsukune in the school infirmary. She suddenly steps to the front of the screen, looks straight at the audience while making a fist and complains "Hey, what the hell is this? I just debuted on the previous episode, can't you let me appear earlier?"
Then the announcer (a bat) appears in the screen saying "Who are you talking to?". Strange, in that the bat constantly appears to be talking to the audience.
Kurumu has broken several more walls after that episode, actually. Since she is a succubus, and succubi have control over reality, it would make sense that she's the only one (other than the bat and maybe her mother) who knows that her world is just an anime.
At the end of episode 11, after Ryuuka has declared that Mariel is her rival for Taro's affection, Grace turns to the audience and says "Is this going to continue?"
La Verite (2nd season) episode 7. The group encounters a series of odd traps.
Ryuuka: Why is this place full of so many lame traps, anyway?
Ikuyo Suzuki: It's as if the producers wanted to show us how unimaginative they are!
In Episode 6 of the Durarara!! anime when Kadota Kyohei explains why they're rescuing Kaztano.
Erika: Who are you talking to?
An episode of the English dub of Sailor Moon altered a line of dialog where Sailor Moon was looking straight at the camera to have her ask the audience to tell her where Luna went. The original script had her worrying to herself.
Another episode in the sub version has Sailor Moon say that Joseph Haydn is the father of music. When Luna says that it's actually Johann Sebastian Bach that has the title, Moon gets embarrassed and says the audience wouldn't have noticed her mistake if Luna hadn't mentioned it.
High School Of The Dead sometimes pokes through the fourth wall, saying that what's happening now would make a great manga. Of course at one point Saya tells Takashi "We get it, you're the main character."
In Neko-de Gomen! when preparing for a school field trip, Yayori packs some feminine supplies. When her father points out what they are, she attacks him claiming that "The readers can hear you!"
In the final chapter of Helen ESP Helen asks Victor if he thinks they're in a story, and Helen says she'd like to meet their readers. Cue dreaming... Hello! How do you do? You're the person who's been reading my story, aren't you? My name is Takahara Helen.
Obake no Q-Taro managed to combine this with Deus ex Machina in its Grand Finale. The heroes are captured and all hope seems to be lost when they are suddenly rescued by Perman. They ask who he is, and he declares himself to be the star of the show. Q-Taro then angrily informs Perman that his show starts next week, and he's arrived a week too early. Sure enough, Perman debuted the following week in Obake no Q-Taro's former time slot.
A minor fourth wall-breaking moment happens in One Piece: in the Laboon arc, Crocus loves to make dramatic glares at people. The third time he does that, the Straw Hats get pissed and tell him to stop doing that, causing him to answer : "Haven't you ever heard of a runnning gag ?".
Brook breaks it during his explanation of why he lacks a shadow.
Brook: "I'll tell you everything now... It has been a long time since I began drifting on this sea... But let me say, my being a skeleton and not having a shadow are completely different things. To be continued in the next chapter."
As early as the intro before the opening in the first episode: even if the anime is a Square Enix-Sunrise collaboration, it would not add mecha or RPG elements to a Slice of Life series.
Intro of episode 3: The main trio recognized the anime aired in winter. They also recognized by starting the story in Summer instead of Spring (when the Japanese school year starts), it misses many cliches of High School anime—but this is a Slice of Life show anyway.
The Distaff Counterparts of the three main boys wondered why those boring boys could have their own anime.
Meta Knight: Oh! It is Fire Dedede, our hero! (turns to camera) ... I would never say that...
In Robotech, the usually formal narrator breaks the fourth wall only twice. The first time is in Wedding Bells, when he humorously comments about Max's nervousness regarding his upcoming date with Mirya: "After all, (laughs), what do you expect from a girl you only met that same morning?". In Season's greetings, he ends the episode by saying "Merry Christmas to all, and to all a safe night."
Haruhichan has this one episode in which, in the begining, Achakura tries to tell her past, but Mr. Kimidori says that the programmers are "turning this into a flashback episode" and asks them to stop.
Also done in some episodes. Then there's one that only exists in the English dub. In one episode, Haruhi was about to throw the dart at Kyon, who begs her to stop because they "have kids watching."
Senjogohara in Bakemonogatari invokes this when her vocal range is called into question.
Senjogahara: I can imitate your voice. So don't worry, leave it to me. After all, my voice actress is excellent.
Yu-Gi-Oh! usually doesn't do this at all, even in the dub. However, in the dub version of Yu-Gi-Oh! 5Ds in Yusei's first duel with Kalin, as Yusei is about to land what appears to be a final blow against Kalin, the Dark Signer says, "Oh no! I'm done for!" Then he looks at the TV screen and adds, "But seriously folks," before he activates a card to save himself. (Of course, this has a bit of Fridge Brilliance to it. Since Kalin is clearly Axe Crazy, this may be the same type of Medium Awareness that insanity gives people like The Joker.
Pandora Hearts does this in every omake, normally having Sharon complain about how little she appears.
Abel Nightroad occasionally supplies the odd fourth wall gag in the Trinity Blood manga, which doesn't take itself as seriously as the original novels and the anime do. He once chastised Esther during chapter six by reminding her that "This is a shoujo manga!", when he thought she was suggesting he was romantically involved with Tres, and he also commented on the romantic tension between Astha and Suleyman during the Queen of the Night arc... by holding up signs to simulate the narration boxes.
The anime of Black Butler has one example of this. In episode 11 of the second season, Grell gets charred. While looking at the forth wall, he says:
''' "Don't worry dear viewers. I shall await your kind letters."
Space Dandy has this in spades in the first episode itself.
The omakes at the end of each volume of Iris Zero always feature the main characters discussing said volume. Also, when discussing how Koyuki would react to being shouted at by Toru, Kuga merely points to a thought bubble depicting her shouting back and says, "Like this."